Genomics Unit

How to access: service request and sample delivery guidelines

All services offered by the Genomics Unit are accessible to all the scientific community. Access is always open and services are performed upon request.

All services and equipment provided by the Genomics Unit are available through the AGENDO web platform.
You can access AGENDO using the following link: https://crg.agendoscience.com/

Sample requirements and shipping guide
Agendo user guide
Quick Agendo sample submission guide

For further information please contact project management at ngs@crg.eu

Service Prices

Prices Genomics

Services offered

Whole and Targeted Genome 

Whole-genome sequencing (WGS) determines the order of all nucleotides in an individual’s DNA and can uncover variation in any part of the human genome, including coding, noncoding, and mitochondrial DNA (mtDNA) regions. In some instances, WGS is the better option because DNA variations outside protein-coding regions can affect gene activity and protein production. We offer several protocols depending on the final objective of the project: 

• WGS-PCR free 
• WGS-PCR
• WGS-Tn5
• WGS-long reads

Targeted Genome identifies short nucleotide and copy number variants across interesting regions of the genome providing a cost-effective alternative to WGS, greater sequencing depth, and producing smaller and more manageable data sets compared to WGS data. There are several approaches as:

• Exome sequencing (WES, 40-60 Mb) focused on the genomic protein coding regions (exons).
• Gene panels or Custom capture sequencing (250 kb-5 Mb) a selected set of genes or areas of interest are studied.
• Amplicon-seq is an approach that enables to analyze genetic variation in specific genomic regions through ultra-deep sequencing of PCR products (amplicons), a common application is sequencing the bacterial 16S rRNA gene across multiple species, a widely used method for phylogeny and taxonomy studies, particularly in diverse metagenomics samples.

Transcriptome

Transcriptome refers to the set of all RNA molecules from protein coding (mRNA) to noncoding RNA, including rRNA, tRNA, lncRNA, pri-miRNA, and others. Bulk RNA-Seq is a method that analyzes pooled RNA from cells or tissues. We can offer several approaches: 

• mRNA-seq where mRNA is selected via oligodT beads from total RNA, so libraries are prepared only from polyadenylated transcripts from samples.
• Ribodepleted RNA-seq analyzes both coding and multiple forms of noncoding RNA for a comprehensive view of the transcriptome.
• Small RNA-seq, a technique to isolate and sequence small RNA species, such as microRNAs (miRNAs) which act in gene silencing and post-transcriptional regulation of gene expression. We provide a wide variety of protocols for standard and low input samples.  

Epigenome

Epigenome corresponds to the changes in gene activity caused by mechanisms other than DNA sequence modifications, including alterations in DNA methylation, DNA-protein interactions, chromatin accessibility, histone modifications, and more. We offer several applications as:

• ChIP-seq is a method for identifying genome-wide DNA binding sites for transcription factors and other proteins. DNA-bound protein is immunoprecipitated using a specific antibody and the bound DNA is then coprecipitated, purified, and sequenced.
• ATAC-seq (assay for transposase-accessible chromatin with sequencing) is a method for determining chromatin accessibility across the genome helping to uncover how chromatin packaging and other factors affect gene expression.
• HiC-seq maps chromatin contacts genome-wide and allows detection of long-range DNA interactions, and it has also been applied to studying in situ chromatin interactions. In this method, DNA-protein complexes are crosslinked with formaldehyde. The sample is fragmented, and the DNA is extracted, ligated, and digested with restriction enzymes. The resulting DNA fragments are PCR-amplified and sequenced. Deep sequencing provides base-pair resolution of the ligated fragments.
• Methyl-seq an approach used to study methylation patterns of DNA. These patterns can be used to identify different cell types in epigenetics and for example, oncology research.

Single Cell and Spatial genomics and transcriptomics

Single-cell sequencing refers to the sequencing of individual cells to obtain genomic, transcriptomic, or multi-omics information at single-cell level. The data you generate with this technology has a much higher resolution than conventional bulk RNA sequencing methods and can reveal details that you would otherwise miss. We offer several protocols depending on the final objective of the project, from microfluidics solutions (10x Genomics) to combinatorial  and plate-based approaches.

• 10X Genomics
• Combinatorial approaches (EasysciRNA-seq, Parse Biosciences, Scale Bio)
• SMARTseq2

Spatial Transcriptomics studies how gene expression is spatially regulated at the tissue level allowing the detection of cellular heterogeneity in tissues, tumours, as well as determine the subcellular distribution of transcripts in various conditions.

• STEREO-seq: spatially-resolved transcriptomic analysis through its proprietary SpaTial Enhanced REsolution Omics-Sequencing (Stereo-seq) technology combines in situ capture with DNB-seq, DNB sequencing is based on lithographically etched chips (patterned arrays) for in situ sequencing.